Mr Sillars said he had met and would be happy to work with former MP Nigel Griffiths, who is leading a Labour campaign to leave the EU in Scotland.
The veteran nationalist and independence campaigner said he believed there could be SNP members who disagreed with the party leadership on Europe but would not speak out for fear of being branded “disloyal”.
First Minister and SNP leader Nicola Sturgeon is strongly in favour of remaining in the EU.
Mr Sillars, husband of the late Margo MacDonald MSP, said: “I certainly met Nigel Griffiths and I’m very impressed by how he has put together a very good Labour Leave campaign in Scotland, but of course this is for Labour Party members and Labour supporters, of which at the moment I am not.
“I’m very happy to co-operate with Nigel. If I can be helpful, I will be helpful.”
Mr Sillars said he had been “really astonished” by the number of SNP members he had spoken to who said that they did not want to remain in the EU.
He said: “There is a tendency if anyone within the party criticises the leadership to be then described as being disloyal. I think that’s a very unhealthy situation inside any democratic political party.
“There may be the situation in which a number of people would like to come out openly and say ‘I don’t agree with the party leadership on the EU’, but prefer not to say so in public. I’m not in that category.
“I’ve said this to SNP members: what I cannot get my head round with the continuing SNP love affair with the EU is for us to go and bat for the EU, an organisation which, during the referendum, told us to get stuffed and would no doubt tell us to get stuffed second time round as well.
“They made sure that the message came through on behalf of Better Together and the Tory government that we would not be allowed automatic entry as a member state.
“Why we should laud an organisation and tell our supporters to vote to remain in it, when it holds us in such contempt, is something I personally don’t understand when there are alternatives for us, which is the European Free Trade Association and the European Economic Area with its treaty with the EU.”
He added: “I think (the EU) is a profoundly undemocratic organisation which has shown a callous disregard for people, in Portugal, Spain and Greece for example.
“They’ve been willing to make people destitute - beggar nations - in pursuit of a single policy to create a United States of Europe irrespective of whether the people want it.”